diff --git a/README.md b/README.md index 8e41ea118..83969d515 100644 --- a/README.md +++ b/README.md @@ -74,7 +74,7 @@ epiparameters #> review." _The Lancet Infectious Diseases_. #> doi:10.1016/S1473-3099(09)70069-6 #> . -#> Distribution: lnorm +#> Distribution: lnorm (days) #> Parameters: #> meanlog: 1.723 #> sdlog: 0.231 @@ -88,7 +88,7 @@ epiparameters #> review." _The Lancet Infectious Diseases_. #> doi:10.1016/S1473-3099(09)70069-7 #> . -#> Distribution: lnorm +#> Distribution: lnorm (days) #> Parameters: #> meanlog: 1.163 #> sdlog: 0.140 @@ -102,7 +102,7 @@ epiparameters #> review." _The Lancet Infectious Diseases_. #> doi:10.1016/S1473-3099(09)70069-8 #> . -#> Distribution: lnorm +#> Distribution: lnorm (days) #> Parameters: #> meanlog: 1.386 #> sdlog: 0.593 @@ -148,7 +148,7 @@ influenza_incubation #> Distribution of the Incubation Periods of Human Avian Influenza A(H7N9) #> Virus Infections." _American Journal of Epidemiology_. #> doi:10.1093/aje/kwv115 . -#> Distribution: weibull +#> Distribution: weibull (days) #> Parameters: #> shape: 2.101 #> scale: 3.839 @@ -230,21 +230,30 @@ or the median and range of the data. This can be done for: ## Contributing to library of epidemiological parameters -If you would like to contribute to the different epidemiological -parameters stored in the `{epiparameter}` package, you can add data to a -public [google -sheet](https://docs.google.com/spreadsheets/d/1eCL3n_woseg5Npu7XD7TcuNoLUIhMBu8ZoLCkVdATUE/edit?usp=sharing). -This spreadsheet contains two example entries as a guide to what fields -can accept. We are monitoring this sheet for new entries that will -subsequently be included in the package. - -Alternatively, parameters can be added to the [JSON file holding the -data](https://github.com/epiverse-trace/epiparameter/blob/main/inst/extdata/parameters.json) -base directly via a Pull Request. - -You can find explanation of accepted entries for each column in the -[data -dictionary](https://github.com/epiverse-trace/epiparameter/blob/main/inst/extdata/data_dictionary.json). +The library of epidemiological parameters that can be loaded by +`{epiparameter}` using the `epiparameter_db()` function is stored in the +[`{epiparameterDB}` R +package](https://github.com/epiverse-trace/epiparameterDB). If you would +like to contribute to the library of epiparameters you can either: + +1. Add data to a public [google + sheet](https://docs.google.com/spreadsheets/d/1eCL3n_woseg5Npu7XD7TcuNoLUIhMBu8ZoLCkVdATUE/edit?usp=sharing). + This spreadsheet contains two example entries as a guide to what + fields are accepted. We are monitoring this sheet for new entries + that will subsequently be included in the package. + +2. Add to the [JSON file holding the + database](https://github.com/epiverse-trace/epiparameterDB/blob/main/inst/extdata/parameters.json) + directly via a Pull Request. See the [contributing + guide](https://github.com/epiverse-trace/.github/blob/main/CONTRIBUTING.md) + for instructions. + +You can find a description of the epidemiological parameter data +structure and contents in the [data +dictionary](https://github.com/epiverse-trace/epiparameterDB/blob/main/inst/extdata/data_dictionary.json). +This documents the valid format and data types to ensure consistency and +accuracy. All entries in the parameter library are automatically +validated against the data dictionary using an GitHub action workflow. ## Help @@ -269,7 +278,7 @@ By contributing to this project, you agree to abide by its terms. citation("epiparameter") #> To cite package 'epiparameter' in publications use: #> -#> Lambert J, Kucharski A, Tamayo C (2024). _epiparameter: Library of +#> Lambert J, Kucharski A, Tamayo C (2025). _epiparameter: Library of #> Epidemiological Parameters with Helper Functions and Classes_. #> doi:10.5281/zenodo.11110881 #> , @@ -280,7 +289,7 @@ citation("epiparameter") #> @Manual{, #> title = {epiparameter: Library of Epidemiological Parameters with Helper Functions and Classes}, #> author = {Joshua W. Lambert and Adam Kucharski and Carmen Tamayo}, -#> year = {2024}, +#> year = {2025}, #> doi = {10.5281/zenodo.11110881}, #> url = {https://epiverse-trace.github.io/epiparameter/}, #> }